A very common pattern is this: Works the first time, doesn't work subsequent times. Change output folder and it will again work the first time, and not after. That is usually due to one of the following:
1) The program doesn't properly handle the condition of an existing file. Being that it's KiCAD, that's entirely possible.
2) The file was opened in a mode that doesn't support overwrite. Again, basic programming error that is entirely likely at this stage of development.
3) The directory permissions allow creating new files but not overwriting existing ones. That's all you. (Are you logged in as admin?)
4) The program did something to the directory or file permissions that prevent further modifications. Possible, but not as likely.
5) Some program on your computer (anti-virus, Gerber viewer, etc.) has the file open, locking it against write operations.